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MajorJohn Sheppard's team are under attack from Wraith Darts, and then sees them wiped out through a mysterious energy beam. They search the planet below, Proculus, who do not have advanced technologies, but Dr.Rodney McKay suspects they are hiding something, especially after the priestess, Chaya Sar comes to Atlantis and has her eyes on Sheppard.

When they land, they find a pre-industrial civilization who know nothing of the Wraith. The people are protected by a being named Athar. The team are taken to meet Athar's priestess, Chaya Sar. McKay blurts out about the weapon protecting the planet but no one has any idea what he's talking about. Sheppard tells him to be quiet. They ask if refugees can be taken in; Chaya consults Athar and says no. Athar understands their cause is righteous, but she must put her own people first. McKay becomes angry. Shepard tries to calm everything down and meets alone with Chaya. He thinks once she gets to know them and understands they are related, she will get Athar to reconsider. Sheppard invites her to come back to Atlantis, and she agrees.

Chaya undergoes some tests at Atlantis. Sheppard shows her the city and talks about Earth. In the control room, Chaya suddenly activates a Biometric Sensor Array, and everyone is surprised to see that she has the Ancient Technology Activation gene. Later, in the conference room, they ask Chaya to accept refugees in exchange for advancements in technology for her civilization, but she declines. She says Athar gives them everything they need. She says further that what her people value most is spiritual knowledge, and asks what they can offer in that regard. They then offer knowledge of Earth's many religions, which she agrees to review.

Later, McKay talks with Sheppard and tells him he feels that something is different about Chaya. Dr.Carson Beckett has found that Chaya is in perfect health, much too perfect for a simple pre-technological society. McKay is suspicious of Chaya, and concerned that Sheppard is forming such a close bond with her. It turns out the new machine that turned on when Chaya touched it can detect aliens, a kind of early warning system for the city. McKay's theory is that it didn't turn on because she had the gene, it turned on because she is an alien and set off an alarm. He can't prove anything either way, but he wants Weir to send her back.

Sheppard decides to take Chaya out to a late night picnic dinner as a show of goodwill. After some talking, they kiss.

Later that night McKay runs into Sheppard in the hallways and tells him of his suspicions about Chaya. Chaya overhears him and walks away.

The next morning, McKay is busy scanning her, trying to prove she is an alien, as Chaya tells everyone that though she is fascinated by their religions, she cannot condone the hate and distrust that the people of Earth display for each other. She points out McKay specifically, especially after his comments of last night. McKay suddenly realizes that she is an Ancient; she confirms his suspicions, and admits that she did not come to offer her help, but out of a romantic interest in Sheppard. She says it is true that she can never offer them sanctuary, and she cannot help them here in Atlantis.

Before the conversation can go any further, she senses that the Wraith are attacking her planet. She turns into her Ascended form and leaves through the Star Gate. Sheppard takes a Jumper and follows her back to Proculus. He takes out a few Darts and Chaya appears beside him and asks him to leave the battle. She turns into her Ascended form again and uses her power to destroy the Wraith forces.

Chaya shares herself with Sheppard

Sheppard comes down to the planet and confronts Chaya. She explains that she is also Athar. Long ago, when the Wraith attacked her planet, she lashed out with one thought and destroyed them all. The Others punished her by restricting her to protecting Proculus only. If she tried anywhere else, she would be stopped. She had been alone for many years until she met Sheppard. After noting that Sheppard will still be permitted to visit her occasionally, she shares herself with him.

(after Chaya delivers the message that Athar cannot help Atlantis)McKay: Well, I think we both knew what you were going to say long before you even went in there.Chaya: (unhappy) We prayed for Athar's guidance.McKay: And what did Athar say? You're hiding behind your religion to justify your complete and utter selfishness.Sheppard: Rodney -McKay: If Athar existed she would be ashamed of herself.

Chaya: What my people value most is spiritual knowledge. What can your culture provide in that regard?Weir: Earth's people don't share a single Spiritual belief - we embrace a number of different religions and philosophies: Christianity, Buddhism, Judaism, Islam -Sheppard: Hinduism ... Kwanzaa.

McKay: Word of caution? The whole Captain Kirk routine is problematic to say the least, let alone morally dubious.Sheppard: What routine?McKay: The romancing of the alien priestess? It's very 1967 of you. Actually, I'm surprised...Sheppard: (interrupting Rodney) If and when anything I do becomes your business...McKay: It becomes my business, Major, when an alien woman who is clearly not who she claims to be has the ranking military officer wrapped around her little finger!Sheppard: Don't go there, McKay.McKay: I'm sorry - I know I'm not normally Mr Sensitive, but you gotta believe me when I say there is something about her. I know it's intangible but I can feel it.Sheppard: I said don't go there!McKay: It's just a matter of time before I prove it, Major. I'm just recommending that in the meantime you keep your...(Chaya Sar appears and he shuts up)

Chaya: I am what you call an Ancient and it is also true that I can never offer your people sanctuary. But you are wrong about as to why I came here.Sheppard: Why did you come here?Chaya: You, John.Sheppard: Me?Chaya: I have lived in solitude for so long that when you asked me to come to Atlantis, I...McKay: Oh my god, he is Kirk!

McKay: All I know is she's not who she's pretending to be.Weir: You know this because…?McKay: What, I'm not allowed to have intuition?Weir: You? No.McKay: Oh.

The first few seconds of the episode, "Childhood's End" show Sheppard's Jumper fly over a lake near a forest. This same footage is recycled in this episode, merely episodes after "Childhood's End", when they fly toward the people of Proculus at 4:18. As far as recycled footage goes - for example: overhead footage of Atlantis, this use of recycled footage could be in violation of canon, for it is extremely unlikely the two locations are exactly the same.

The equipment pack seen behind MajorJohn Sheppard in the Puddle Jumper when he comes to help with the orbital battle displays the "Atlantis" logo of the television series' promotional titles, rather than the 'Pegasus & chevron' symbol of the fictional Atlantis expedition.

When he first arrives on the planet, Sheppard's jacket bears the usual Atlantis and US flag patches on the arms, however by the time he talks to Chaya Sar the patches are gone. Later, as Dr.Elizabeth Weir welcome Chaya to Atlantis, the patches are back. It seems odd that after displaying them to an entire village, he'd remove them for a meeting with only one person, then replace them for that same person to see.

Chaya's blood pressure was recorded at 130 over 70. This is actually considered pre-hypertensive since the first number, the systolic pressure, is over 120 and is not a sign of perfect health at all. The optimal blood pressure for adults is actually around 115/80 mmHg. Despite this, it has been made abundantly clear that Lantean physiology is somewhat noticeably different. It is unknown why Carson did not notice this, but it is entirely plausible that Chaya intentionally deceived Carson.

Dr. Grodin states that he has been working on the Ancient "logarithms". The correct term for what he meant is algorithms, procedures a computer uses to calculate values.

When Sheppard takes a Jumper back to the planet after it is revealed Chaya is an ancient, the gate dialing scene clearly switches from prop to digital effects with the chevrons changing appearance.

McKay states that because Darts are present there must be a Hive Ship around. Darts are also capable of using the Stargate, a fact which he is well aware of.